+ puts( " " + PRG_NAME + ".rb [options] <hmmscan outputfile> [outputfile]" )
+ puts()
+ puts( " options: -" + DELIMITER_OPTION + "=<s> : column delimiter for outputfile, default is TAB" )
+ puts( " -" + I_E_VALUE_THRESHOLD_OPTION + "=<f>: i-E-value threshold, default is no threshold" )
+ puts( " -" + PARSE_OUT_DESCRIPITION_OPTION + " : parse query description (in addition to query name)" )
+ puts( " -" + IGNORE_DUF_OPTION + " : ignore DUFs" )
+ puts( " -" + HMM_FOR_PROTEIN_OUTPUT + "=<s> : HMM for protein architectures summary" )
+ puts( " -" + FS_E_VALUE_THRESHOLD_OPTION + "=<f>: E-value threshold for full protein sequences, only for protein architectures summary" )
+ puts( " -" + SPECIES_OPTION + "=<s> : species for protein architectures summary" )
+ puts()
+ puts( " [next step in standard analysis pipeline: d2f.rb]")
+ puts()
+ puts( "Examples:" )
+ puts()
+ puts( " " + "hmmscan --max --domtblout P53_hmmscan_#{Constants::PFAM_V_FOR_EX}_10 -E 10 Pfam-A.hmm P53_ni.fasta" )